VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 27 2007 - 12:42:49 CDT

Hi,
  If you have the DSSP secondary structure in the PDB file, you can
use this script to parse it and apply it, replacing whatever STRIDE
has already calculated:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmd_use_pdb_ss/

I don't currently have a script for reading the output of DSSP directly.
You could write one however, in a manner similar to the way the script
above works.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 27, 2007 at 12:04:54PM +0200, pascal.baillod_at_epfl.ch wrote:
>
> Hello!
>
> I am currently using stride or pdb based secondary structure definitions, but
> would be very glad to use dssp definitions to depict my proteins in vmd. Is
> there any script like the stride-based one that can do this? I thank you very
> much for your help!!
>
> I actually already sent a note on this topic in 2005, and was just wondering if
> there's any news since then..
>
> Thanks a lot in advance!!
>
> Pascal
>
>
>
> *******************************************************************************
> Pascal Baillod (PhD student)
> *******************************************************************************
> Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322
> Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320
> Laboratory of Computational Chemistry and Biochemistry pascal.baillod_at_epfl.ch
> Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch
> CH-1015 Lausanne
> ******************************************************************************* 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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